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Detailed information for vg0323603573:

Variant ID: vg0323603573 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 23603573
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

CAATTGGCTTCGAAAGTGGGGGCATGGATGCAATTATCCCTTTTTGTTTTTCTTCTCTCTTATACTGGGTCTCCCGTCAGCTTTTAAAATATAGATAGAT[A/G]
GATTAAATGATCATTCTACTCTTTTACATATACCCCATAATAAATAAAAAGAAAAAAAAGATGACAGGCCAGCCAACATTGTTTCTATCTTTCCCTTAAA

Reverse complement sequence

TTTAAGGGAAAGATAGAAACAATGTTGGCTGGCCTGTCATCTTTTTTTTCTTTTTATTTATTATGGGGTATATGTAAAAGAGTAGAATGATCATTTAATC[T/C]
ATCTATCTATATTTTAAAAGCTGACGGGAGACCCAGTATAAGAGAGAAGAAAAACAAAAAGGGATAATTGCATCCATGCCCCCACTTTCGAAGCCAATTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.20%	48.50%	0.25%	0.00%	NA
All Indica	2759	20.40%	79.20%	0.36%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.07%	0.00%	NA
Aus	269	77.70%	22.30%	0.00%	0.00%	NA
Indica I	595	30.90%	68.40%	0.67%	0.00%	NA
Indica II	465	18.90%	80.90%	0.22%	0.00%	NA
Indica III	913	11.00%	88.70%	0.33%	0.00%	NA
Indica Intermediate	786	24.30%	75.40%	0.25%	0.00%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	60.00%	38.90%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0323603573	A -> G	LOC_Os03g42410-LOC_Os03g42420	intergenic_region ; MODIFIER	silent_mutation	Average:56.693; most accessible tissue: Callus, score: 83.577	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0323603573	NA	1.11E-07	mr1045	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323603573	NA	2.31E-07	mr1053	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323603573	NA	3.20E-06	mr1058	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323603573	2.32E-06	NA	mr1106	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323603573	NA	2.00E-06	mr1106	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323603573	NA	6.09E-12	mr1195	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323603573	NA	9.48E-06	mr1285	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323603573	NA	3.14E-13	mr1329	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323603573	NA	2.53E-06	mr1408	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323603573	NA	7.30E-06	mr1568	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323603573	NA	3.76E-09	mr1663	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323603573	NA	1.24E-07	mr1748	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0323603573	NA	9.35E-08	mr1785	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251